Your sentence is almost correct but can be made clearer and grammatically smoother. Here's a better version:
"Mangrove trees drink salty water through their roots. They put the extra salt into their leaves, which they shed later."
Explanation:
- We add a comma before "which" because it introduces extra information about the leaves.
- "Shed later" means the leaves fall off after storing the extra salt.
This way, the sentence is clear and easy to understand.